wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15353/suppl/GSE15353%5FSTAT1%5Fhg18%5FIFNg%5Fht11%2Epeaks%2Etxt wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15353/suppl/GSE15353%5FSTAT1%5Fhg18%5FIFNg%5Fht11%2Ewig wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15353/suppl/GSE15353%5FSTAT1%5Fhg18%5FUnstimulated%5Fht11%2Epeaks%2Etxt wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15353/suppl/GSE15353%5FSTAT1%5Fhg18%5FUnstimulated%5Fht11%2Ewig
less -SN GSE15353_STAT1_hg18_IFNg_ht11.peaks.txt
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz gunzip hg18ToHg38.over.chain.gz
# Code cell supp 1 mapgenes <- NULL for (i in 1:nrow(STAT1_unstim_peaks_hg38)) { if(i %in% seq(1, nrow(STAT1_unstim_peaks_hg38), 100)){ message(i) } genes <-getBM(attributes = c("hgnc_symbol", "description", "ensembl_gene_id","chromosome_name", "start_position", "end_position", "strand"), filters = c("chromosome_name", "start", "end"), values = list(gsub("chr", "", STAT1_unstim_peaks_hg38$chr[i]), STAT1_unstim_peaks_hg38$start[i] - 10000, STAT1_unstim_peaks_hg38$end[i] + 10000), mart = ensembl) if(nrow(genes)>0){ genes$peak_coordinates <- paste0(STAT1_unstim_peaks_hg38$chr[i], ":", STAT1_unstim_peaks_hg38$start[i], "-", STAT1_unstim_peaks_hg38$end[i]) genes$peak_ID <- STAT1_unstim_peaks_hg38$ID[i] mapgenes <- rbind(mapgenes, genes) } } STAT1_unstim_peaks_genes20kb_hg38 <- mapgenes save(STAT1_unstim_peaks_genes20kb_hg38, file = "STAT1_unstim_peaks_genes20kb_hg38.RData")# Code cell supp 2 mapgenes <- NULL for (i in 1:nrow(STAT1_ifng_peaks_hg38)) { if(i %in% seq(1, nrow(STAT1_ifng_peaks_hg38), 100)){ message(i) } genes <-getBM(attributes = c("hgnc_symbol", "description", "ensembl_gene_id","chromosome_name", "start_position", "end_position", "strand"), filters = c("chromosome_name", "start", "end"), values = list(gsub("chr", "", STAT1_ifng_peaks_hg38$chr[i]), STAT1_ifng_peaks_hg38$start[i] - 10000, STAT1_ifng_peaks_hg38$end[i] + 10000), mart = ensembl) if(nrow(genes)>0){ genes$peak_coordinates <- paste0(STAT1_ifng_peaks_hg38$chr[i], ":", STAT1_ifng_peaks_hg38$start[i], "-", STAT1_ifng_peaks_hg38$end[i]) genes$peak_ID <- STAT1_ifng_peaks_hg38$ID[i] mapgenes <- rbind(mapgenes, genes) } } STAT1_ifng_peaks_genes20kb_hg38 <- mapgenes save(STAT1_ifng_peaks_genes20kb_hg38, file = "STAT1_ifng_peaks_genes20kb_hg38.RData")